Inhibition of NEAT1 for treatment of solid tumors

ABSTRACT

The application relates to the field of cancer, particularly to the field of solid tumors. It was found that a particular long non-coding RNA (lncRNA), NEAT1, an essential architectural component of nuclear paraspeckles, is required for the survival of cancer, but not that of normal, non-transformed, cells. Inhibition of NEAT1 reduces cell viability of cancer cells and induces apoptosis. These data identify NEAT1 as a novel therapeutic target for treatment of solid tumors.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a national phase entry under 35 U.S.C. §371 ofInternational Patent Application PCT/EP2015/052663, filed Feb. 9, 2015,designating the United States of America and published in English asInternational Patent Publication WO 2015/118156 A1 on Aug. 13, 2015,which claims the benefit under Article 8 of the Patent CooperationTreaty to European Patent Application Serial No. 14154284.5, filed Feb.7, 2014.

TECHNICAL FIELD

The present application relates to the field of cancer, particularly tothe field of solid tumors. It was found that a particular longnon-coding RNA (lncRNA), NEAT1, an essential architectural component ofnuclear paraspeckles, is required for the survival of cancer, but notthat of normal, non-transformed cells. Inhibition of NEAT1 reduces cellviability of cancer cells and induces apoptosis. These data identifyNEAT1 as a novel therapeutic target for treatment of solid tumors.

BACKGROUND

p53 is the archetypal tumor suppressor, but still a lot remains to belearned about the mechanisms by which p53 exerts its tumor suppressorfunction. Many target genes have been described, both direct andindirect targets, transcription factors, both protein coding genes andnon-coding genes (e.g., miRNAs). However, although it is generallyaccepted that p53 is a master apoptosis regulator, it is still unknownhow p53 makes the switch from arrest/survival to apoptosis. As p53 insome cases even seems to help tumorigenesis, it would be advantageous toidentify mechanisms by which p53 stimulates or prevents apoptosis,particularly of cancer cells.

Moreover, since cancer cells have developed an increased ability tosurvive in sub-optimal environment, even irrespective of the presence orabsence of wild-type p53, it would be advantageous to identify targetsthat can modulate cell survival downstream of p53. Most preferably, suchtargets would allow selective modulation of the pathway in cancer cells,so that these cells can be selectively killed.

BRIEF SUMMARY

Using RNAseq and ChIPseq experiments, NEAT1 was identified as a directtarget gene of p53. NEAT1 is an abundant nuclear long non-coding RNAthat functions as an essential architectural component of nuclearparaspeckles. Although the function of paraspeckles remains unclear,transfection studies indicate that they modulate gene transcriptionand/or mRNA translation through sequestration of specific transcriptionfactors and/or edited mRNAs, respectively.

To investigate the physiological role of paraspeckles in vivo, mice thatlack NEAT1 were generated. NEAT1 knockout (KO) mice are viable and haveno apparent phenotype except for a defect in pubertal mammary glandbranching morphogenesis along with reduced lobular-alveolar developmentduring pregnancy and lactation capacity.

Despite the previous observation that NEAT1 expression and paraspecklesformation increases upon passages, it is shown herein thatNEAT1-deficient Mouse Embryonic Fibroblasts (MEFs) do not exhibit anysignificant growth defects indicating that NEAT1 and paraspeckles aredispensable for the proliferation and survival of normal,non-transformed cells. In contrast, cultured cancer cells are dependenton NEAT1 expression for their survival. Knocking-down NEAT1 usingLNA-modified antisense oligonucleotides drastically decreases the numberof paraspeckles, the metabolic activity and viability of a wide varietyof cancer cell lines.

Although the lncRNA NEAT1 plays critical roles in vivo during mammarygland morphogenesis, its expression is, by and large, dispensable duringadulthood. Together with the observation that NEAT1 is required for thesurvival of cancer, but not normal/non-transformed cells, these dataidentify NEAT1 as a therapeutic target for cancer therapy.

Provided are inhibitors of functional expression of the NEAT1 gene. Suchinhibitors can act at the DNA level or at the RNA (i.e., gene product)level. As NEAT1 is a non-coding gene, there is no protein product forthis gene.

According to a further aspect, the inhibitors of functional expressionof NEAT1 are provided for use as a medicament. According to yet furtheraspects, the inhibitors of functional expression of NEAT1 are providedfor use in treatment of cancer, in particular, for use in treatment ofsolid tumors. In still further embodiments, the inhibitors are providedfor use in treatment of carcinoma (i.e., cancers derived from epithelialcells). According to alternative embodiments, the inhibitors areprovided for use in treatment of cancers selected from the group ofbreast cancer, skin cancer, osteosarcoma, colorectal cancer, andneuroblastoma. According to very specific embodiments, the skin canceris non-melanoma skin cancer, typically selected from BCC (basal cellcarcinoma) or SCC (squamous cell carcinoma).

This is equivalent to saying that methods of treating a solid tumor in asubject in need thereof are provided, the method comprisingadministering an inhibitor of functional expression of NEAT1 to thesubject. Likewise, it is equivalent to providing methods of treatingcarcinoma, or methods of treating a cancer selected from the group ofbreast cancer, skin cancer, osteosarcoma, colorectal cancer, andneuroblastoma, wherein an inhibitor of functional expression of NEAT1 isprovided to the subject.

The nature of the inhibitor is not vital to the disclosure, as long asit inhibits the functional expression of the NEAT1 gene. According tospecific embodiments, the inhibitor is selected from a gapmer, an shRNA,an siRNA, a CRISPR, a TALEN, a Zinc-finger nuclease or a small molecule.According to specific embodiments, the inhibitor is administered to, oris targeted to, cancer cells (such as solid tumor cells).

According to alternative, but not exclusive, specific embodiments, theinhibitor selectively induces apoptosis in cancer cells. Thisparticularly implies that it induces apoptosis in cancer (e.g.,carcinoma) cells, but not in normal (non-transformed) similar cells(e.g., epithelial cells). According to further specific embodiments, theinhibitor induces apoptosis independent of p53 status, e.g., independentwhether p53 has particular mutations or not, or independent of itsexpression levels.

It is shown herein that NEAT1 inhibition interferes with DNA repairpathways, particularly with the double-strand repair mechanisms such ashomologous recombination (HR) and non-homologous end joining (NHEJ).This means that cells in which NEAT1 is inhibited will be particularlysensitive to inhibition of the remaining single-strand repair pathways(excision repair pathways), such as base excision repair (BER), whereascells in which NEAT1 is not inhibited will be a lot less sensitive tothis treatment.

Thus, according to particular embodiments, combinations of an inhibitorof a DNA excision repair enzyme with an inhibitor of functionalexpression of NEAT1 are provided for use in the treatment of cancer.This is envisaged to induce synthetic lethality in cells.

According to specific embodiments, the inhibitor of a DNA excisionrepair enzyme is an inhibitor of a DNA base excision repair enzyme.According to further specific embodiments, the inhibitor of a DNA baseexcision repair enzyme is a PARP inhibitor.

Furthermore, it is shown herein that NEAT1 controls mitochondriadynamics and that this could also contribute to its oncogenicactivities. NEAT1 is required for expression of MFF, which, in turn,modulate mitochondria fission. Loss of NEAT1 leads to a robust decreasein MFF expression and eventually to swollen mitochondria and increasedsensitivity to oxidative stress and/or oncogenic stress. Targeting NEAT1makes the cancer cells extremely sensitive to oxidative stress. Thus,according to particular embodiments, combinations of an agent thatincreases oxidative stress with an inhibitor of functional expression ofNEAT1 are provided for use in the treatment of cancer. This is alsoenvisaged to induce synthetic lethality in cells. Examples of suchagents that increase oxidative stress are known in the art and include(but are not limited to), e.g., rotenone, H₂O₂, tBHP, and okadaic acid.

According to a similar aspect, methods of treating cancer are provided,comprising administering an inhibitor of functional expression of NEAT1to a subject in need thereof, which methods may further entailadministering an inhibitor of a DNA base excision repair enzyme. Thiscan be done as a combination treatment (i.e., concomitant orsimultaneous administration) or can be done by separate administrationof the compounds, but particularly by subsequent administration (i.e.,within a limited time frame of each other, so that both inhibitors aresimultaneously active in the subject).

According to a further aspect, methods are provided that may identifywhether a tumor is suitable for treatment with an inhibitor offunctional expression of NEAT1. These methods typically have thefollowing steps:

-   -   Determining whether expression of NEAT1 is increased in the        tumor or a sample of tumor cells; and    -   Establishing whether the tumor is suitable for treatment,        wherein increased expression is indicative of suitability for        treatment.

Typically, the tumor will be a solid tumor. Thus, the methods may entaila first step of providing a sample of (solid) tumor cells. Thedetermining step may occur purely in vitro, i.e., without a stepinteracting on the human or animal body.

According to particular embodiments, the tumor is a carcinoma. Accordingto alternative embodiments, the tumor is selected from breast cancer,skin cancer, osteosarcoma, colorectal cancer, and neuroblastoma.

According to specific embodiments, when it is established that the tumoris suitable for treatment, the methods may further comprise a step ofadministering an inhibitor of functional expression of NEAT1 to thesubject in which the tumor is present. This is in order to treat thetumor.

These inhibitors may be further combined with, e.g., an inhibitor of aDNA excision repair enzyme, or an agent that increases oxidative stress.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIG. 1 provides evidence that NEAT1 is a direct p53 target gene in thebreast cancer cell line MCF-7. RNA-seq and p53 ChIPseq experiments havebeen carried out in MCF-7 cells following exposure to the MDM2antagonist Nutlin3a for 24 hours. The NEAT1 locus is shown and theRNA-seq peaks in blue are shown in untreated (Control) cells and inNutlin3a-treated cells for 24 hours (two biological replicates areshown), the increase in intensity of the peaks from 0 (control) to 24hours indicate that Nutlin3a induces transcription of NEAT1. Thep53-ChIP peaks are shown in green; these peaks indicate that p53 isdirectly recruited to the NEAT1 promoter upon Nutlin3a exposure.

FIGS. 2A-2G. Both NEAT1 transcripts (NEAT1_1 and the long isoformNEAT1_2) are induced by Nutlin3a in various p53 wild-type human cancercell lines. The effect is p53-dependent.

FIGS. 3A and 3B. Nutlin3a induces paraspeckles formation in ap53-dependent manner. FIG. 3A: MCF-7 cells were exposed to Nutlin3a (for24 hours) and paraspeckles formation (red dots) was assessed byFISH-analysis with a NEAT1-specific probe set. Nuclei werecounter-stained with DAPI (Blue). FIG. 3B: Quantification ofparaspeckles formation in MCF-7 cells exposed to Nutlin3a before (mock)and after transfection of the cells with a control/scramble gapmer (scr)or gapmers targeting the NEAT1 transcripts (gap4 and gap6).

FIGS. 4A-4F. NEAT1 is induced in human and mouse cells exposed to lowstress conditions including exposure to the inducer of senescenceaurora-kinase inhibitor AZD1152-HQPA (AZD; FIG. 4A), low doses ofRotenone (Rot; FIG. 4B) that promotes oxidative stress, low doses ofdoxorubicin (Doxo, FIG. 4C) and replicative stress-induced damage (RS;FIG. 4D). NEAT1 is not significantly induced in cells exposed toapoptotic-inducing stress level such as high doses of Doxo (FIG. 4E) andhigh doses of irradiation (12 Gy; FIG. 4F).

FIG. 5. NEAT1 paraspeckles are formed in vivo in response to oncogenicstress. Panels A-D: Paraspeckles form upon oncogenic stress afterDMBA/TPA treatment. Nuclear staining with DAPI (blue), staining of theparaspeckles using RNA-FISH of NEAT1 (red), and co-staining of thesuprabasal layers of the epidermis with Keratin 1 (green). White dottedlines delineate the basement membrane of the epidermis. No paraspecklesare observed in normal epidermis 48 hours after topical DMBA treatment(Panel A). Paraspeckles are present and gradually more abundant ininterfollicular epidermis hyperplasia (Panel B), epidermal papilloma(Panel C) and differentiated squamous cell carcinoma (Panel D). PanelsE-H: Paraspeckles form upon oncogenic stress in the K19 CreERKRasLSL-G12D genetic mouse model (Lapouge et al., 2011). Nuclearstaining with DAPI (blue), staining of the paraspeckles using RNA-FISHof NEAT1 (red) and co-staining of the basal and suprabasal layers of theepidermis with Keratin 5 (cyan). White dotted lines delineate thebasement membrane of the epidermis. Staining of the epidermis is shown,1 week (Panel E), 1 month (Panel F) and 2 months (Panel G) afterTamoxifen administration or upon occurrence of epidermis hyperplasia,and 4 months after Tamoxifen administration (Panel H).

FIGS. 6A-6C. Tumor development is significantly altered in NEAT1 KO(−/−) mice exposed to a two-stage chemically induced carcinogenesisprotocol. (FIG. 6A) Number of papillomas per mouse (n=31) after 8 monthsof DMBA/TPA treatment; significance determined by unpaired two-tailedt-test. (FIG. 6B) Percentage of mice with squamous cell carcinomas inthe same experiment (n=31, p-value 0.0072, chi-square test). (FIG. 6C)Representative pictures of the mice are shown.

FIGS. 7A-7F. NEAT1 is required for primary cells immortalization. NEAT1expression in induced in mouse embryonic fibroblasts (MEFs) uponNutlin3a exposure (FIG. 7A) and replicative passaging on a 3T3 protocol(FIG. 7B). Although the growth of NEAT1 KO MEFs is comparable towild-type controls at early passages (FIG. 7C), NEAT1 KO cells enterapoptosis and cannot be immortalized at late passages (FIGS. 7D-7F) incontrast to the WT MEFs. Since immortalization of MEFs is invariablyassociated with inactivation of the p53 pathway, this result indicatesthat NEAT1 and p53 may be synthetically lethal.

FIGS. 8A-8D. NEAT1 KD reduces the cell viability of human cancer celllines. Gapmers 4 and 5 (gap 4 and 5) were used to knock-down theexpression of all NEAT1 isoforms, and Gapmer 6 (gap 6) to specificallyKD expression of the long isoform, in a series of cancer cell lines.Transfection of gaps 4 and 5 causes a robust decrease in NEAT1expression (FIG. 8A) and paraspeckles formation (FIG. 8B), and inductionof apoptosis as measured using a caspase 3/7 glow assay (FIG. 8C) and byFACS analysis. Transfection of gap 4, gap 5 and gap 6 all decrease MCF-7growth significantly as measured using a WST1-assay (FIG. 8D).

FIGS. 9A-9C. Knock-down of NEAT1 impairs HR and NHEJ DNA repair (FIG.9A) but not Alt-NHEJ or SSA (FIG. 9B). (FIG. 9C) Top panel showsefficient KD of the different NEAT1 isoforms with the gapmers, as shownby relative RNA levels. SCR: scrambled control. Blue bars, all NEAT1isoforms. Green bars, long NEAT1 isoform. Low panel shows NEAT1 KD cellsaccumulate more damage than control cells upon exposure of U2OS cells tolow concentrations of the DNA-damaging agent bleomycin. This result isconsistent with a reduced ability of NEAT1 KD cells to repair DNAdamage.

FIGS. 10A and 10B. NEAT1 KD leads to a dramatic decrease in MFFexpression. (FIG. 10A) This panel shows efficient KD of the differentNEAT1 isoforms with the gapmers, as shown by relative RNA levels 24hours and 48 hours post-transfection. N1C: scrambled control (red bars);N1KD NEAT1_1 and NEAT1_2 KD (orange bars). (FIG. 10B) MFF mRNA relativeexpression in various cancer cell lines upon NEAT1 KD. This figure showsthat MFF transcription is highly dependent upon NEAT1 expression.

FIGS. 11A and 11B. NEAT1 KD in cancer cells leads to an increase inbasal p53 activity and sensitizes p53 wild-type cancer cells to p53reactivation therapy. (FIG. 11A) Western blotting showing that the p53functionality is exacerbated in NEAT1 KD cells following exposure toNutlin3a (in MCF7 cells) and consequently Nutlin3a-induced apoptosis isincreased (as exemplified by an increase in PARP cleavage) upon NEAT1KD. (FIG. 11B) mRNA expression levels of the p53-canonical target gene,p21, is increased in NEAT1 KD cells, in particular, upon exposure toNutlin3a; this data confirm an increase in p53 transcriptional activityin these experimental conditions.

FIG. 12. Model of how NEAT1 upregulation in response to low, chronicand/or oncogenic stress contributes to cell survival in pre-neoplasticcells. When exposed to the same stress, cells that lack NEAT1 will dieas a result of mitochondrial defects and compromised DNA repair.

DETAILED DESCRIPTION Definitions

This disclosure will be described with respect to particular embodimentsand with reference to certain drawings but the invention is not limitedthereto but only by the claims. Any reference signs in the claims shallnot be construed as limiting the scope. The drawings described are onlyschematic and are non-limiting. In the drawings, the size of some of theelements may be exaggerated and not drawn on scale for illustrativepurposes. Where the term “comprising” is used in the present descriptionand claims, it does not exclude other elements or steps. Where anindefinite or definite article is used when referring to a singularnoun, e.g., “a,” “an,” or “the,” this includes a plural of that noununless something else is specifically stated.

Furthermore, the terms “first,” “second,” “third,” and the like, in thedescription and in the claims, are used for distinguishing betweensimilar elements and not necessarily for describing a sequential orchronological order. It is to be understood that the terms so used areinterchangeable under appropriate circumstances and that the embodimentsdescribed herein are capable of operation in other sequences thandescribed or illustrated herein.

The following terms or definitions are provided solely to aid in theunderstanding of the disclosure. Unless specifically defined herein, allterms used herein have the same meaning as they would to one skilled inthe art. Practitioners are particularly directed to Sambrook et al.,Molecular Cloning: A Laboratory Manual, 2^(nd) ed., Cold Spring HarborPress, Plainsview, N.Y. (1989); and Ausubel et al., Current Protocols inMolecular Biology (Supplement 47), John Wiley & Sons, New York (1999),for definitions and terms of the art. The definitions provided hereinshould not be construed to have a scope less than understood by a personof ordinary skill in the art.

The term “NEAT1” as used herein refers to the gene nuclear paraspeckleassembly transcript 1 (sometimes also referred to as nuclear enrichedabundant transcript 1, and previously sometimes known as TncRNA), GeneID: 283131 in humans, as well as the mRNA that is transcribed from thegene. As it is a non-protein coding gene, there is no protein product.The human gene has different transcripts (or splice variants), thenomenclature of which is not entirely consistent. As used herein,NEAT1_1 refers to Genbank accession number NR 028272 (with a transcriptlength of 3756 bp), the term NEAT1_2 is used for the longest transcriptof over 20 kb (22743 bp for GenBank accession HG503867; transcript IDENST00000501122 in Ensembl (but there referred to as NEAT1_1) or 21760bp for UCSC link uc010rog.2). Other reported transcripts include, e.g.,GenBank accession HG503866 (transcript ID ENST00000499732 in Ensembl(but there referred to as NEAT1_2) with a length of 1745 bp), accessionno. EF177379 (3729 bp), NEAT1_202 (transcript ID ENST00000601801, 1457bp) and NEAT1_201 (transcript ID ENST00000384994, 100 bp miRNA).

Both the NEAT1_1 and NEAT1_2 transcripts are lincRNA (large intergenicnon-coding RNAs).

Unless specifically mentioned otherwise, the term NEAT1 encompasses thedifferent isoforms. Fragments of NEAT1 are also envisaged, as long asthey are functionally active (for instance, if they are able to formparaspeckles). According to particular embodiments, the NEAT1 geneproduct refers to the long transcript(s), particularly the >20 kbtranscripts, that are a structural part of paraspeckles (i.e.,particularly NEAT1_2).

With “functional expression” of NEAT1 is meant the transcription and/ortranslation of functional gene product. For non-protein coding geneslike NEAT1, “functional expression” can be deregulated on at least twolevels. First, at the DNA level, e.g., by absence or disruption of thegene, or lack of transcription taking place (in both instances,preventing synthesis of the relevant gene product). The lack oftranscription can, e.g., be caused by epigenetic changes (e.g., DNAmethylation) or by loss of function mutations. A “loss-of-function” or“LOF” mutation as used herein is a mutation that prevents, reduces orabolishes the function of a gene product as opposed to again-of-function mutation that confers enhanced or new activity on aprotein. LOF can be caused by a wide range of mutation types, including,but not limited to, a deletion of the entire gene or part of the gene,splice site mutations, frame-shift mutations caused by small insertionsand deletions, nonsense mutations, missense mutations replacing anessential amino acid and mutations preventing correct cellularlocalization of the product. Also included within this definition aremutations in promoters or regulatory regions of the NEAT1 gene if theseinterfere with gene function. A null mutation is an LOF mutation thatcompletely abolishes the function of the gene product. A null mutationin one allele will typically reduce expression levels by 50%, but mayhave severe effects on the function of the gene product. Note thatfunctional expression can also be deregulated because of a gain offunction mutation: by conferring a new activity on the protein, thenormal function of the protein is deregulated, and less functionallyactive protein is expressed.

Second, at the RNA level, e.g., by lack of efficient translation takingplace, for example, because of destabilization of the mRNA (e.g., by UTRvariants) so that it is degraded before translation occurs from thetranscript, or by lack of efficient transcription, e.g., because amutation introduces a new splicing variant.

The term “status” as used in the application with regard to a particularprotein, specifically tumor-associated proteins (e.g., p53 status, Mycstatus), refers to the mutational status and/or the expression of theseparticular proteins. Typically, the term is used in the sense“irrespective of” or “independent of” status, meaning that an effect isobserved irrespective of expression levels of, or presence of mutationsin, the particular protein (e.g., p53, Myc status).

“Long non-coding RNAs” (long ncRNAs, lncRNA) as used herein arenon-protein coding transcripts longer than 200 nucleotides. A particularclass of lncRNA are long intergenic ncRNAs (lincRNA), referring to longnon-coding RNAs that are transcribed from non-coding DNA sequencesbetween protein-coding genes.

A “solid tumor” or “neoplasm” as used herein refers to an abnormal massof tissue as a result of abnormal growth or division of cells.Typically, these tumors are malignant. The term does not encompass bloodtumors (leukemia, lymphoma, multiple myeloma). These tumors aretypically characterized by epigenetic abnormalities (chromosomaltranslocations) that are uncommon in solid tumors.

“Carcinoma” as used herein refers to cancers derived from epithelialcells.

An “inhibitor of a DNA base excision repair enzyme” as used hereinrefers to a substance that can interfere with the base excision repairfunction of the gene product, either at the DNA level (by inhibiting theformation of the relevant gene product, i.e., by preventing orinterfering with transcription), at the RNA level (by neutralizing ordestabilizing mRNA to prevent or interfere with translation) or at theprotein level (by neutralizing or inhibiting the protein involved inBER). It is particularly envisaged that the inhibitor is a PARPinhibitor, as such inhibitors are well characterized. Most particularlyenvisaged are inhibitors of PARP-1 and/or of PARP-2, as these enzymesare the PARPs most actively involved in BER. However, inhibitors ofother PARPs may be useful as well. In this regard, recent publicationssuggest that the PARP inhibitor iniparib, which is explicitly envisagedfor use, inhibits PARPs other than PARP-1 and 2, particularly PARP-5 and6 (J. Ji, M. P. Lee, M. Kadota, et al., Pharmacodynamic and pathwayanalysis of three presumed inhibitors of poly (ADP-ribose) polymerase:ABT-888, AZD 2281, and BSI201, Proceedings of the 102nd Annual Meetingof the American Association for Cancer Research 2011 Apr. 2-6, Orlando,Fla. AACR. 2011, Abstract nr 4527; K. A. Maegley, P. Bingham, J. H.Tatlock, et al., All PARP inhibitors are not equal: an in vitromechanistic comparison of PF-01367338 to iniparib, J. Clin. Oncol. 2011,29 (suppl; abstr e13576); R. A. Nagourney, K. R. Kenyon, F. R.Francisco, et al., Functional analysis of PARP inhibitors AZD 2281 andBSI-201 in human tumor primary cultures: a comparison of activity andexamination of synergy with cytotoxic drugs, J. Clin. Oncol. 2011, 29(suppl; abstr e13599)).

The present application is the first to show that NEAT1 expression canbe dispensed with in normal, non-transformed cells, while its expressionis important for the survival of cancer cells. Consequently, inhibitionof NEAT1 lncRNA can be used to selectively induce apoptosis in cancercells, particularly solid tumor cells, most particularly carcinomacells.

Accordingly, provided are inhibitors of functional expression of theNEAT1 gene. Such inhibitors can act at the DNA level, or at the RNA(i.e., gene product) level. As NEAT1 is a non-coding gene, there is noprotein product for this gene.

If inhibition is to be achieved at the DNA level, this may be done usinggene therapy to knock-out or disrupt the target gene. As used herein, a“knock-out” can be a gene knockdown or the gene can be knocked out by amutation such as a point mutation, an insertion, a deletion, aframeshift, or a missense mutation by techniques known in the artincluding, but not limited to, retroviral gene transfer. Another way inwhich genes can be knocked out is by the use of zinc finger nucleases.Zinc-finger nucleases (ZFNs) are artificial restriction enzymesgenerated by fusing a zinc finger DNA-binding domain to a DNA-cleavagedomain. Zinc finger domains can be engineered to target desired DNAsequences that enable zinc-finger nucleases to target unique sequencewithin a complex genome. By taking advantage of endogenous DNA repairmachinery, these reagents can be used to precisely alter the genomes ofhigher organisms. Other technologies for genome customization that canbe used to knock out genes are meganucleases and TAL effector nucleases(TALENs, Cellectis bioresearch). A TALEN® is composed of a TALE DNAbinding domain for sequence-specific recognition fused to the catalyticdomain of an endonuclease that introduces double-strand breaks (DSB).The DNA binding domain of a TALEN® is capable of targeting with highprecision a large recognition site (for instance, 17 bp). Meganucleasesare sequence-specific endonucleases, naturally occurring “DNA scissors,”originating from a variety of single-celled organisms such as bacteria,yeast, algae and some plant organelles. Meganucleases have longrecognition sites of between 12 and 30 base pairs. The recognition siteof natural meganucleases can be modified in order to target nativegenomic DNA sequences (such as endogenous genes).

Another recent genome editing technology is the CRISPR/Cas system, whichcan be used to achieve RNA-guided genome engineering. CRISPR is anacronym for Clustered Regularly Interspaced Short Palindromic Repeats,i.e., DNA loci that contain multiple, short, direct repetitions of basesequences. “Cas” stands for CRISPR ASsociated genes. Plasmids with casgenes and specifically designed CRISPR regions can be used to modify ahost genome at any location (Hale et al., Molecular Cell 45 (3):292-302(2012); Cong et al., Science 339 (6121):819-823 (2013); Mali et al.,Science 339 (6121):823-826 (2013)).

Gene inactivation, i.e., inhibition of functional expression of thegene, may, for instance, also be achieved through the creation oftransgenic organisms expressing antisense RNA, or by administeringantisense RNA to the subject. An antisense construct can be delivered,for example, as an expression plasmid, which, when transcribed in thecell, produces RNA that is complementary to at least a unique portion ofthe cellular NEAT1 lncRNA.

A more rapid method for the inhibition of gene expression is based onthe use of shorter antisense oligomers consisting of DNA, or othersynthetic structural types such as phosphorothiates,2′-0-alkylribonucleotide chimeras, locked nucleic acid (LNA), peptidenucleic acid (PNA), or morpholinos. With the exception of RNA oligomers,PNAs and morpholinos, all other antisense oligomers act in eukaryoticcells through the mechanism of RNase H-mediated target cleavage. PNAsand morpholinos bind complementary DNA and RNA targets with highaffinity and specificity, and thus act through a simple steric blockadeof the RNA translational machinery, and appear to be completelyresistant to nuclease attack. An “antisense oligomer” refers to anantisense molecule or anti-gene agent that comprises an oligomer of atleast about 10 nucleotides in length. In some embodiments, an antisenseoligomer comprises at least 15, 18, 20, 25, 30, 35, 40, or 50nucleotides. Antisense approaches involve the design of oligonucleotides(either DNA or RNA, or derivatives thereof) that are complementary to anRNA encoded by polynucleotide sequences of NEAT1. Antisense RNA may beintroduced into a cell to inhibit translation of a complementary mRNA bybase pairing to it and physically obstructing the translation machinery.This effect is, therefore, stoichiometric. Absolute complementarity,although preferred, is not required. A sequence “complementary” to aportion of an RNA, as referred to herein, means a sequence havingsufficient complementarity to be able to hybridize with the RNA, forminga stable duplex. In the case of double-stranded antisense polynucleotidesequences, a single strand of the duplex DNA may thus be tested, ortriplex formation may be assayed. The ability to hybridize will dependon both the degree of complementarity and the length of the antisensepolynucleotide sequence. Generally, the longer the hybridizingpolynucleotide sequence, the more base mismatches with an RNA it maycontain and still form a stable duplex (or triplex, as the case may be).One skilled in the art can ascertain a tolerable degree of mismatch byuse of standard procedures to determine the melting point of thehybridized complex. Antisense oligomers should be at least 10nucleotides in length, and are preferably oligomers ranging from 15 toabout 50 nucleotides in length. In certain embodiments, the oligomer isat least 15 nucleotides, at least 18 nucleotides, at least 20nucleotides, at least 25 nucleotides, at least 30 nucleotides, at least35 nucleotides, at least 40 nucleotides, or at least 50 nucleotides inlength. A related method uses ribozymes instead of antisense RNA.Ribozymes are catalytic RNA molecules with enzyme-like cleavageproperties that can be designed to target specific RNA sequences.Successful target gene inactivation, including temporally andtissue-specific gene inactivation, using ribozymes has been reported inmouse, zebrafish and fruitflies. RNA interference (RNAi) is a form ofpost-transcriptional gene silencing. The phenomenon of RNA interferencewas first observed and described in Caenorhabditis elegans whereexogenous double-stranded RNA (dsRNA) was shown to specifically andpotently disrupt the activity of genes containing homologous sequencesthrough a mechanism that induces rapid degradation of the target RNA.Several reports describe the same catalytic phenomenon in otherorganisms, including experiments demonstrating spatial and/or temporalcontrol of gene inactivation, including plant (Arabidopsis thaliana),protozoan (Trypanosoma bruceii), invertebrate (Drosophila melanogaster),and vertebrate species (Danio rerio and Xenopus laevis). The mediatorsof sequence-specific messenger RNA degradation are small interferingRNAs (siRNAs) generated by ribonuclease III cleavage from longer dsRNAs.Generally, the length of siRNAs is between 20-25 nucleotides (Elbashiret al. (2001) Nature 411:494 498). The siRNA typically comprise a senseRNA strand and a complementary antisense RNA strand annealed together bystandard Watson Crick base pairing interactions (hereinafter “basepaired”). The sense strand comprises a nucleic acid sequence that isidentical to a target sequence contained within the target mRNA. Thesense and antisense strands of the present siRNA can comprise twocomplementary, single-stranded RNA molecules or can comprise a singlemolecule in which two complementary portions are base paired and arecovalently linked by a single-stranded “hairpin” area (often referred toas shRNA). The term “isolated” means altered or removed from the naturalstate through human intervention. For example, an siRNA naturallypresent in a living animal is not “isolated,” but a synthetic siRNA, oran siRNA partially or completely separated from the coexisting materialsof its natural state is “isolated.” An isolated siRNA can exist insubstantially purified form, or can exist in a non-native environmentsuch as, for example, a cell into which the siRNA has been delivered.

The siRNAs of the disclosure can comprise partially purified RNA,substantially pure RNA, synthetic RNA, or recombinantly produced RNA, aswell as altered RNA that differs from naturally occurring RNA by theaddition, deletion, substitution and/or alteration of one or morenucleotides. Such alterations can include addition of non-nucleotidematerial, such as to the end(s) of the siRNA or to one or more internalnucleotides of the siRNA, including modifications that make the siRNAresistant to nuclease digestion.

One or both strands of the siRNA of the disclosure can also comprise a3′ overhang. A “3′ overhang” refers to at least one unpaired nucleotideextending from the 3′ end of an RNA strand. Thus, in one embodiment, thesiRNA of the disclosure comprises at least one 3′ overhang of from oneto about six nucleotides (which includes ribonucleotides ordeoxynucleotides) in length, preferably from one to about fivenucleotides in length, more preferably, from one to about fournucleotides in length, and particularly preferably, from about one toabout four nucleotides in length.

In the embodiment in which both strands of the siRNA molecule comprise a3′ overhang, the length of the overhangs can be the same or differentfor each strand. In a most preferred embodiment, the 3′ overhang ispresent on both strands of the siRNA, and is two nucleotides in length.In order to enhance the stability of the present siRNAs, the 3′overhangs can also be stabilized against degradation. In one embodiment,the overhangs are stabilized by including purine nucleotides, such asadenosine or guanosine nucleotides.

Alternatively, substitution of pyrimidine nucleotides by modifiedanalogues, e.g., substitution of uridine nucleotides in the 3′ overhangswith 2′ deoxythymidine, is tolerated and does not affect the efficiencyof RNAi degradation. In particular, the absence of a 2′ hydroxyl in the2′ deoxythymidine significantly enhances the nuclease resistance of the3′ overhang in tissue culture medium.

The siRNAs of the disclosure can be targeted to any stretch ofapproximately 19 to 25 contiguous nucleotides in any of the target NEAT1RNA sequences (the “target sequence”), of which examples are given inthe application. Techniques for selecting target sequences for siRNA arewell known in the art. Thus, the sense strand of the present siRNAcomprises a nucleotide sequence identical to any contiguous stretch ofabout 19 to about 25 nucleotides in the target mRNA.

The siRNAs of the disclosure can be obtained using a number oftechniques known to those of skill in the art. For example, the siRNAscan be chemically synthesized or recombinantly produced using methodsknown in the art. Preferably, the siRNA of the disclosure are chemicallysynthesized using appropriately protected ribonucleosidephosphoramidites and a conventional DNA/RNA synthesizer. The siRNA canbe synthesized as two separate, complementary RNA molecules, or as asingle RNA molecule with two complementary regions. Commercial suppliersof synthetic RNA molecules or synthesis reagents include Proligo(Hamburg, Germany), Dharmacon Research (Lafayette, Colo., USA), PierceChemical (part of Perbio Science, Rockford, Ill., USA), Glen Research(Sterling, Va., USA), ChemGenes (Ashland, Mass., USA) and Cruachem(Glasgow, UK).

Alternatively, siRNA can also be expressed from recombinant circular orlinear DNA plasmids using any suitable promoter. Suitable promoters forexpressing siRNA of the disclosure from a plasmid include, for example,the U6 or H1 RNA pol III promoter sequences and the cytomegaloviruspromoter. Selection of other suitable promoters is within the skill inthe art. The recombinant plasmids of the disclosure can also compriseinducible or regulatable promoters for expression of the siRNA in aparticular tissue or in a particular intracellular environment. ThesiRNA expressed from recombinant plasmids can either be isolated fromcultured cell expression systems by standard techniques, or can beexpressed intracellularly, e.g., in breast tissue or in neurons.

The siRNAs of the disclosure can also be expressed intracellularly fromrecombinant viral vectors. The recombinant viral vectors comprisesequences encoding the siRNAs of the disclosure and any suitablepromoter for expressing the siRNA sequences. Suitable promoters include,for example, the U6 or H1 RNA pol III promoter sequences and thecytomegalovirus promoter. Selection of other suitable promoters iswithin the skill in the art. The recombinant viral vectors of thedisclosure can also comprise inducible or regulatable promoters forexpression of the siRNA in the tissue where the tumor is localized.

As used herein, an “effective amount” of the siRNA is an amountsufficient to cause RNAi-mediated degradation of the target mRNA, or anamount sufficient to inhibit the progression of metastasis in a subject.RNAi-mediated degradation of the target mRNA can be detected bymeasuring levels of the target mRNA or protein in the cells of asubject, using standard techniques for isolating and quantifying mRNA orprotein as described above.

One skilled in the art can readily determine an effective amount of thesiRNA of the disclosure to be administered to a given subject, by takinginto account factors such as the size and weight of the subject; theextent of the disease penetration; the age, health and sex of thesubject; the route of administration; and whether the administration isregional or systemic. Generally, an effective amount of the siRNA of thedisclosure comprises an intracellular concentration of from about 1nanomolar (nM) to about 100 nM, preferably from about 2 nM to about 50nM, more preferably from about 2.5 nM to about 10 nM. It is contemplatedthat greater or lesser amounts of siRNA can be administered.

It has been shown that morpholino antisense oligonucleotides inzebrafish and frogs overcome the limitations of RNase H-competentantisense oligonucleotides, which include numerous non-specific effectsdue to the non-target-specific cleavage of other mRNA molecules causedby the low stringency requirements of RNase H. Morpholino oligomers,therefore, represent an important new class of antisense molecule.Oligomers of the disclosure may be synthesized by standard methods knownin the art. As examples, phosphorothioate oligomers may be synthesizedby the method of Stein et al. (1988), Nucleic Acids Res. 16:3209 3021),methylphosphonate oligomers can be prepared by use of controlled poreglass polymer supports (Sarin et al. (1988), Proc. Natl. Acad. Sci.U.S.A. 85:7448-7451). Morpholino oligomers may be synthesized by themethod of Summerton and Weller, U.S. Pat. Nos. 5,217,866 and 5,185,444.

Another particular form of antisense RNA strategy are gapmers. A gapmeris a chimeric antisense oligonucleotide that contains a central block ofdeoxynucleotide monomers sufficiently long to induce RNase H cleavage.The central block of a gapmer is flanked by blocks of 2′-O modifiedribonucleotides or other artificially modified ribonucleotide monomerssuch as bridged nucleic acids (BNAs) that protect the internal blockfrom nuclease degradation. Gapmers have been used to obtainRNase-H-mediated cleavage of target RNAs, while reducing the number ofphosphorothioate linkages. Phosphorothioates possess increasedresistance to nucleases compared to unmodified DNA. However, they haveseveral disadvantages. These include low binding capacity tocomplementary nucleic acids and non-specific binding to proteins thatcause toxic side-effects limiting their applications. The occurrence oftoxic side-effects, together with non-specific binding causingoff-target effects, has stimulated the design of new artificial nucleicacids for the development of modified oligonucleotides that provideefficient and specific antisense activity in vivo without exhibitingtoxic side-effects. By recruiting RNase H, gapmers selectively cleavethe targeted oligonucleotide strand. The cleavage of this strandinitiates an antisense effect. This approach has proven to be a powerfulmethod in the inhibition of gene functions and is emerging as a popularapproach for antisense therapeutics. Gapmers are offered commercially,e.g., LNA™ longRNA GapmeRs by Exiqon, or MOE Gapmers by Isispharmaceuticals. MOE gapmers or “2′MOE Gapmers” are an antisensephosphorothioate oligonucleotide of 15-30 nucleotides, wherein all ofthe backbone linkages are modified by adding a sulfur at thenon-bridging oxygen (phosphorothioate) and a stretch of at least tenconsecutive nucleotides remain unmodified (deoxy sugars) and theremaining nucleotides contain an O′-methyl O′-ethyl substitution at the2′ position (MOE). Exemplary gapmers for NEAT1 inhibition are listed inthe Examples.

According to a further aspect, the inhibitors of functional expressionof NEAT1 are provided for use as a medicament. According to yet furtheraspects, the inhibitors of functional expression of NEAT1 are providedfor use in treatment of cancer, in particular, for use in treatment ofsolid tumors. In still further embodiments, the inhibitors are providedfor use in treatment of carcinoma (epithelial cancers).

Typical examples of carcinomas include, but are not limited to:epithelial neoplasms (ICD 8010-8045), squamous cell neoplasms (ICD8050-8080), such as squamous cell carcinoma, basal cell neoplasms (ICD8090-8110), such as basal cell carcinoma, transitional cell carcinomas(ICD 8120-8130), adenocarcinomas (ICD 8140-8380), such asadenocarcinoma, linitis plastic, vipoma, cholangiocarcinoma,hepatocellular carcinoma, adenoid cystic carcinoma, renal cellcarcinoma, adnexal and skin appendage neoplasms (ICD 8390-8420),mucoepidermoid neoplasms (ICD 8430-8439), cystic, mucinous and serousneoplasms (ICD 8440-8490), ductal, lobular and medullary neoplasms (ICD8500-8540), acinar cell neoplasms (ICD 8550-8559), and complexepithelial neoplasms (ICD 8560-8580).

Examples of organ sites of carcinomas include, but are not limited to,lung, breast, prostate, colon and rectum, pancreas and ovaries.

According to alternative embodiments, the inhibitors are provided foruse in treatment of cancers selected from the group of breast cancer,skin cancer, osteosarcoma, colorectal cancer, and neuroblastoma.According to very specific embodiments, the skin cancer is non-melanomaskin cancer. According to further specific embodiments, the skin canceris selected from BCC or SCC.

According to very specific embodiments, the cancer envisaged fortreatment is not a blood tumor. For example, the cancer is not selectedfrom the group consisting of leukemia, lymphoma and multiple myeloma.Blood tumors (or liquid tumors) are typically characterized bychromosomal translocations that are not often observed in solid tumors,leading to different diagnosis and treatment paradigms. Also, as thesetumor cells typically circulate, local administration of therapy is muchmore difficult.

According to similar embodiments, methods of treating cancer in asubject in need thereof are provided, comprising administering aninhibitor of functional expression of NEAT1 to the subject. Here also,particularly envisaged cancers to be treated are solid tumors. In stillfurther embodiments, methods are provided for treating carcinoma in asubject in need thereof. The cancers to be treated are as elaboratedabove.

The nature of the NEAT1 inhibitor is not vital to the disclosure, aslong as it inhibits the functional expression of the NEAT1 gene.According to specific embodiments, the inhibitor is selected from aninhibitory RNA technology (such as a gapmer, an shRNA, an siRNA), aCRISPR, a TALEN, or a Zinc-finger nuclease. According to specificembodiments, the inhibitor is administered to, or is targeted to, cancercells (such as solid tumor cells).

According to alternative, but not exclusive, specific embodiments, theinhibitor selectively induces apoptosis in cancer cells. Thisparticularly implies that it induces apoptosis in cancer cells, but notin normal (non-transformed) similar cells. Similar in this context meanscells from the same tissue or origin, but non-transformed, e.g.,epithelial cells as compared to carcinoma cells.

According to further specific embodiments, the inhibitor inducesapoptosis independent of p53 status, e.g., independent whether p53 hasparticular mutations or not, or independent of its expression levels.

Although inhibition of NEAT1 expression is enough to induce apoptosis ofcancer cells (see Examples section), combination treatments of NEAT1inhibitors with other anti-cancer agents are envisaged as well. As NEAT1inhibition interferes with DNA repair pathways (particularly thehomologous recombination and non-homologous end-joining repairpathways), particularly envisaged combinations are with inhibitors ofother repair pathways, such as the base excision repair pathway.

Thus, according to particular embodiments, combinations of an inhibitorof a DNA excision repair enzyme with an inhibitor of functionalexpression of NEAT1 are provided for use in the treatment of cancer.Likewise, methods for treating cancer are provided to treat a subject inneed thereof, in which a combination of an inhibitor of a DNA excisionrepair enzyme with an inhibitor of functional expression of NEAT1 isadministered to the subject.

According to a further aspect, methods are provided that may identifywhether a cancer is suitable for treatment with an inhibitor offunctional expression of NEAT1. These methods typically have thefollowing steps:

-   -   Determining whether expression of NEAT1 is increased in the        cancer or a sample of cancer cells; and    -   Establishing whether the tumor is suitable for treatment,        wherein increased expression is indicative of suitability for        treatment.

“Determining expression” may encompass processes such as detecting ormeasuring the presence of gene products, or determining the expressionlevels, i.e., the (relative or absolute) amount of gene product present.Determining expression may be done qualitatively (i.e., whether or notthere is expression in a sample) and/or quantitatively (determining theamount of expression, or expression levels). Most typically, expressionwill be done quantitatively, in order to be able to compare expressionlevels. Determining expression may involve comparison with a positivecontrol (e.g., to assess whether gene products can be detected in thesample, in particular, whether the detection method works), a negativecontrol or a blank (typically to assess whether no false positive signalis being generated), one or more standards (either internal or externalstandards, typically to allow more accurate quantification), or acombination thereof. The positive control may additionally oralternatively be an internal positive control, typically a gene productknown to be present in the sample (e.g., to assess whether gene productscan be detected in the sample, in particular, whether the detectionmethod works or whether gene products are indeed present in the sample).Detection of expression and/or activity is well known in the art, and askilled person is capable of choosing appropriate controls and/orstandards.

Note that determining the presence or expression of NEAT1 meansdetermining presence or expression of at least one isoform. It isexplicitly envisaged to determine presence or expression of the total ofall RNA isoforms of NEAT1, or one or more specific RNAs.

As mentioned, determining the amount of a gene may involve comparisonwith one or more controls or standards. Typically, this will be done toestablish whether the levels of the gene product are altered, mostparticularly increased. As used herein, “altered levels” of a geneproduct may mean either “increased levels” or “decreased levels” of agene product, which is typically assessed versus a control. The skilledperson is capable of picking the most relevant control. This may, forinstance, depend on the particular gene product, the nature of thecancer studied, the sample(s) that is/are available, and so on. Suitablecontrols include, but are not limited to, expression in cells of asubject that is cancer-free (optionally from the same subject whenhe/she was still healthy), or a set of clinical data on average geneproduct levels in healthy volunteers. It may also be an artificiallygenerated expression standard, e.g., as used in “real” quantitative PCR.As is evident from the foregoing, the control may be from the samesubject or from one or more different subjects or derived from clinicaldata. Optionally, the control is matched for, e.g., sex, age, etc.

With “increased levels of a gene product,” as mentioned herein, is meantlevels that are higher than are normally present. Typically, this can beassessed by comparing to the control. According to particularembodiments, increased levels of a gene product are levels that are 10%,20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 90%, or even up to 100%higher than those of the control. According to further particularembodiments, it means that the gene product is present, whereas itnormally (or in control) is absent, or at virtually non-detectablelevels. In other words, in these embodiments, detecting the presence ofa particular gene product is equivalent to detecting increased levels ofthe gene product. According to yet further particular embodiments, itmeans that the gene product is present, whereas in the majority of cellsamples from tumor-free individuals, taken as a control, it is not. Theskilled person will appreciate that the exact levels by which a geneproduct needs to be higher in order to allow a reliable and reproduciblediagnosis may depend on the type of tumor tested, of which isoform thelevels are assessed and the natural variability of these levels.However, assessing the increase itself is fairly straightforward, sinceit only requires routine techniques.

Instead of looking at increased levels compared to a control with normallevels, the skilled person will appreciate that an alternative,comparing to a control with high levels (e.g., a sample of a tumor inwhich NEAT1 is highly expressed), can also be done. Thus, if the geneproduct levels measured in the cells or cell sample are similar to thoseof a suitable “control” obtained from a subject with a tumor sensitiveto treatment with NEAT1 inhibitors, this may be considered equivalent toincreased gene product levels compared to a positive control, and becorrelated to sensitivity of the cells to treatment with inhibitors offunctional NEAT1 expression. In the other case, if gene product levelsare significantly lower than those of a control with high levels ofNEAT1, this can be used to establish insensitivity to treatment withinhibitors of DNA base excision repair enzymes.

For “decreased levels” of a gene product compared to a positive ornegative control, the considerations about increased levels of a geneproduct apply mutatis mutandis. Of course, gene product levels may becompared to both a negative and a positive control in order to increaseaccuracy of the diagnosis.

Assessing decreased levels of NEAT1 can, e.g., be done to monitor thesuccess of NEAT1 inhibition, to check whether the therapy is successful.

According to particular embodiments, determining the expression (or theincreased expression) of NEAT1 is done by determining the expression ofthe long isoform of NEAT1.

Of note, since NEAT1 is a major structural component of paraspeckles,determining the expression of NEAT1 can be done by assessing thepresence and/or the number of paraspeckles in the cells of the sample.An increase in number of paraspeckles is equivalent to an increase infunctional NEAT1 expression, whereas a decrease (or absence) ofparaspeckles indicates decreased expression of NEAT1.

As the methods comprise a step of determining expression of NEAT1 in thecancer or a sample of cancer cells, the methods thus may entail a firststep of providing a sample of cancer cells. The determining step mayoccur purely in vitro, i.e., without a step interacting on the human oranimal body.

According to particular embodiments, the cancer is a solid tumor.According to alternative embodiments, the tumor is a carcinoma.According to further alternative embodiments, the cancer is selectedfrom breast cancer, skin cancer, osteosarcoma, colorectal cancer, andneuroblastoma.

According to specific embodiments, when it is established that the tumoris suitable for treatment, the methods may further comprise a step ofadministering an inhibitor of functional expression of NEAT1 to thesubject in which the tumor is present in order to treat the tumor.

As already mentioned, the NEAT1 expression levels can be monitored afteradministration of the inhibitor to check whether the functionalexpression of NEAT1 decreases (typically compared to the situation priorto treatment). This can be correlated to success of the therapy.

According to alternative particular embodiments, the methods maycomprise a step of administering a combination of an inhibitor offunctional expression of NEAT1 and an inhibitor of a base excisionrepair enzyme, such as a PARP inhibitor.

It is to be understood that although particular embodiments, specificconfigurations as well as materials and/or molecules, have beendiscussed herein for cells and methods according to this disclosure,various changes or modifications in form and detail may be made withoutdeparting from the scope and spirit of this invention. The followingexamples are provided to better illustrate particular embodiments, andthey should not be considered limiting the application. The applicationis limited only by the claims.

EXAMPLES Example 1 NEAT is a Direct Target Gene of p53, and it isInduced in Different Cell Types

By performing RNAseq and ChlPseq analysis, NEAT1 was confirmed as adirect target gene of p53 (FIG. 1).

Treatment of the breast cancer cell line MCF-7 with Nutlin3A, a specificantagonist of the master negative regulator of p53, MDM2, transcriptionof NEAT1, and particularly the long isoform NEAT1_2, is upregulated asillustrated by the increased intensity of the RNA-seq peaks (in blue inFIG. 1). This upregulation is mediated through the recruitment of p53 tothe NEAT1 promoter as illustrated by the increase intensity of thep53-ChIP-seq peaks (green in FIG. 1).

The effect of Nutlin3A on NEAT1 expression was evaluated in severalother cell lines, including U2OS (osteosarcoma, FIG. 2A), A459 (lungcarcinoma, FIG. 2B), human ES cells (FIG. 2C), and an immortalized humanfibroblast cell line (BJ, FIG. 2D). p21, a p53 target gene was used ascontrol, as this should be upregulated by Nutlin3A exposure. It could beshown that Nutlin3A indeed induces expression of NEAT1 in thesedifferent cell lines. Both isoforms are affected, with the effect beingstronger for the longer isoform (NEAT1_2).

Next, it was evaluated whether this effect is p53-dependent. Knockingdown p53 in MCF-7 by shRNA (p53 shRNA sequence:GACTCCAGTGGTAATCTACTTCAAGAGAGTAGATTACCACTGGAGTCTTTTTT; SEQ ID NO: 1)abolishes the upregulation of NEAT1, indicating that Nutlin-mediatedNEAT1 induction is indeed p53-dependent (FIG. 2F). Comparable resultswere obtained in a Neuroblastoma cell line (NGP; FIG. 2G).

Thus, the induction of NEAT1 is both p53-dependent and not limited tobreast cancer cell lines.

To differentiate between the different isoforms of NEAT, the followingstrategy was used. All qPCRs labeled NEAT1 or NEAT1_1 were done withprimers targeting the region of +/−2200 bp. The knock-down probeslabeled as such also target the region between 2000 and 3756 bp. TheRNA-FISH probeset used is made up of a large set of oligos targetingregion 1-3756 bp. The primers and knock-down probes labeled NEAT1_2 (thelong transcript) target a region of +/−21300 bp. The RNA-FISH probes(again a set of oligos) target the portion from 3800-11700 bp to avoiddetection of shorter isoforms.

The gapmers used to inhibit NEAT1 were the following:

NEAT1-Gapmer4 (SEQ ID NO: 2) GACGTAACAGAATT NEAT1-Gapmer5 (SEQ ID NO: 3)TAAGCACTTTGGAAAG NEAT1-Gapmer6 (SEQ ID NO: 4) CTCACACGTCCATCT

Gapmers 4 and 5 inhibit both the long and short isoform of NEAT1; gapmer6 is specific for the long isoform.

NEAT1 induction in response to Nutlin can be seen in the colorectalcancer cell line HCT116, but not in an isogenic p53 KO HCT116 cell line(FIG. 2E), again confirming that the nutlin-induced expression of NEAT1is p53-mediated. The p53-NEAT1 pathway is also conserved in the mouse asNutlin induces expression of NEAT1 in early passage (P3) mouse embryonicfibroblasts (MEFs) (not shown).

The upregulation of NEAT1 by Nutlin also has functional consequences:Nutlin induces paraspeckles formation in MCF-7 cells (FIGS. 3A and 3B).

Paraspeckles (red) are detected by RNA-FISH in the nuclei (blue; DAPIstaining) of MCF-7 following Nutlin exposure; the effect is dramaticallyattenuated when NEAT1 (both isoforms or only long isoform) is inhibited(FIGS. 3A and 3B, images treated with gapmer 4 or 6). The relativenumber of paraspeckles per cell for non-treated (NT) or Nutlin3a-treatedcells is shown in FIG. 3B. A similar observation in MCF-7 cells treatedwith p53 shRNA confirms again that this induction is p53-dependent (datanot shown). Thus, p53 stimulates the formation of paraspeckles in thesecells.

A comparable result has been obtained in the immortalized human diploidfibroblast cell line, BJ (data not shown). Transfection of the cellswith LNA-gapmers 4 and 6, both targeting NEAT1, also decrease theformation of paraspeckles, confirming previous studies showing thatparaspeckles formation is dependent on the expression of NEAT1.

Example 2 NEAT1 is Induced by Different Forms of Low and/or ChronicStress, but not by High Stress

The data indicate that whereas a clear p53-dependent induction of NEAT1and paraspeckles formation is observed in response to low/chronic stresslevels, no induction is seen in response to acute stress levels (FIGS.4A-4F).

NEAT1 is upregulated in different conditions of low chronic stress: itis induced in the melanoma cells Mel 501 undergoing senescence inresponse to exposure to the aurora kinase inhibitor, AZD (FIG. 4A); itis induced in BJ cells in response to oxidative stress induced byexposure of the cells to rotenone (FIG. 4B); it is also induced inresponse to low dose of Doxorubicin (FIG. 4C) and during replicationstress (RS) in the Wi38 (lung fibroblast) cell line (FIG. 4D) and mouseNEAT1 in induced in MEFs upon passages in culture (data not shown). Ithas been shown that p53 is induced in MEFs during passages as a responseto increasing oxidative stress levels generated by culturing of thecells in normoxic conditions. As a side note, NEAT1 is also foundupregulated in pigmented/thickened epidermal keratinocytes, anepithelial cell type (not shown). This is in line with chronic stresscaused by UV radiation.

Remarkably, the induction of NEAT1 expression occurs only in response tolow dose of doxorubicin, but not significantly to higher dose (5 μM,FIG. 4E). The same is true for cells that are exposed to high doses ofirradiation (FIG. 4F).

Apart from low and chronic stress, the effect of oncogenic stress wasevaluated by treatment with DMBA/TPA (7,12-Dimethylbenz[a]anthracene and12-O-tetradecanoylphorbol-13-acetate) as carcinogens (FIG. 5).

Example 3 Generation of NEAT1 KO Mice Shows that they do not have MajorGrowth Defects

To examine the physiological role of NEAT1 and paraspeckles in vivo,mice that lack NEAT1 were generated. In line with an earlier report(Nakagawa et al., 2011), NEAT1 knock-out (KO) mice are viable and haveno immediate apparent phenotype. However, we observed a defect inpubertal mammary gland branching morphogenesis along with reducedlobular-alveolar development during pregnancy and lactation capacity(data not shown). See Standaert et al., RNA, 2014 for a completedescription of this work.

Example 4 NEAT1 Inhibition Selectively Affects Survival of Cancer, butnot of Normal Cells

Although NEAT1 KO mice show no apparent growth defects, tumordevelopment is significantly altered in NEAT1 KO (−/−) mice exposed to atwo-stage chemically induced carcinogenesis protocol (DMBA/TPA). NEAT1inhibition results in significantly less papilloma formation in thismodel (FIGS. 6A-6C). Heterozygous (NEAT1+/−) mice show an intermediatephenotype.

To further study the effect of loss of NEAT1 on cell growth andsurvival, NEAT1 KO MEFs were explanted in culture. These cells show nooverall growth defect at early passages and enter senescence just liketheir WT counterparts. Remarkably, however, the NEAT1 KO cellseventually die (after many passages in culture) and cannot beimmortalized, in contrast to the WT MEFs (FIGS. 7A-7F). This indicatesthat NEAT1 has a pro-survival function in chronic stress cultureconditions, and that its inhibition induces apoptosis when cellsaccumulate, possibly immortalizing/transforming mutations. Sinceimmortalization of MEFs is invariably associated with inactivation ofthe p53 pathway, this result indicates that NEAT1 and p53 may besynthetically lethal.

To further extend the anti-oncogenic effects observed in NEAT1 KO mice,NEAT1 was inhibited in different cancer cells using LNA-gapmers. Thesedifferent gapmers can efficiently knockdown NEAT1 (either both long andshort isoforms (gap 4, gap 5) or only the long isoform (gap 6). The KDefficiency of these gapmers are illustrated in FIGS. 8A and 9C. It couldbe shown that, in different cancer cell types, NEAT1 KD inducesparaspeckles (FIG. 8B), reduces cell viability and induces apoptosis, asmeasured by increased caspase 3 and 7 activity and FACS analysis (FIG.8C). Metabolic activity of cancer cells and thus growth is also severelyaffected (FIG. 8D). For U2OS cells, detachment of the cells from theirplastic support was observed (data not shown).

Example 5 NEAT1 Inhibition Impairs DNA Repair Pathways and MitochondrialFission, and Sensitizes Cancer Cells to p53 Reactivation Therapy

One of the possible mechanisms underlying the NEAT1-induced cellularsurvival is activation of DNA repair. Thus, effect of NEAT1 inhibitionon DNA repair pathways was evaluated. It was found that knock-down ofNEAT1 impairs HR and NHEJ DNA repair (FIG. 9A), but not Alt-NHEJ or SSArepair (FIG. 9B). Consequently, additional inhibition of thenon-inhibited, base excision repair (BER) pathway will give rise tosynthetic lethality.

To confirm the hypothesis that NEAT1 inhibition interferes with DNArepair, U2OS cells were exposed to different concentrations of theDNA-damaging agent bleomycin. In NEAT1-inhibited cells, DNA damage (asmeasured by γH2AX intensity) is indeed increased (FIG. 9C, last threepanels). Thus, DNA repair is severely impaired in NEAT1 KD cells. Ofnote, the longest transcript is about 8× less expressed than the shorterforms; thus, it is expected that NEAT1_2 gapmer does not lead to KD whendetecting expression with NEAT1 primers, since KD efficiency ofgapmerNEAT1_2 is about 50%) (NEAT1=hNeat1; NEAT1_2=hNeat1_2).

Another mechanism that may underlie the apoptotic effects observed uponNEAT1 inhibition are mitochondrial defects, as NEAT1 and the associatedparaspeckles control mitochondria dynamics. It could be observed thatNEAT1 inhibition leads to a dramatic decrease in MFF (Mitochondrialfission factor) expression (FIGS. 10A and 10B).

Further, NEAT1 KD leads to an increase in basal p53 activity, as shownby Western blot (FIG. 11A) and by induction of p53 transcriptionalactivity (FIG. 11B).

Thus, a model is proposed (FIG. 12) in which NEAT1 helps cellularsurvival (e.g., of pre-neoplastic cells) by keeping normal mitochondrialfission, DNA damage and p53 in check in response to low/chronic oroncogenic stress. Loss of NEAT1 severely compromises the viability ofpre-neoplastic cells in response to these stress conditions.

REFERENCES

-   Nakagawa S., T. Naganuma, G. Shioi, and T. Hirose. Paraspeckles are    subpopulation-specific nuclear bodies that are not essential in    mice. J. Cell. Biol. 2011; 193(1):31-9.-   Standaert L., C. Adriaens, E. Radaelli, A. Van Keymeulen, C.    Blanpain, T. Hirose, S. Nakagawa, and J. C. Marine. The long    noncoding RNA Neatl is required for mammary gland development and    lactation. RNA 2014 December; 20(12):1844-9.

The invention claimed is:
 1. A combination comprising: an amount of aninhibitor of a DNA base excision repair enzyme useful in the combinationin the treatment of cancer, and an amount of an inhibitor of functionalexpression of NEAT1 acting at the RNA level, wherein the inhibitor isselected from the group consisting of a gapmer an antisenseoligonucleotide, an shRNA or, and an siRNA that hybridizes to NEAT1 RNAin a cell.
 2. The combination of claim 1, wherein the inhibitor of a DNAbase excision repair enzyme is a PARP inhibitor.
 3. A method of treatinga solid tumor in a subject in need thereof, the method comprising:inhibiting functional expression of NEAT1 in the subject byadministering to the subject the combination of claim 1 an inhibitorselected from the group consisting of an antisense oligonucleotide, anshRNA, and an siRNA that is complementary to NEAT1 RNA.
 4. A method ofidentifying a solid tumor suitable for treatment with an inhibitor offunctional expression of NEAT1 , wherein the inhibitor is thecombination of claim 1, the method comprising: determining whetherexpression of NEAT1 is increased in the tumor or in a sample of tumorcells therefrom, relative to NEAT1 expression in non-tumor tissue, thusestablishing whether the tumor is suitable for treatment, whereinincreased expression is indicative of suitability for treatment.
 5. Themethod according to claim 4, wherein the solid tumor is a carcinoma. 6.The method according to claim 4, wherein expression of the long isoformof NEAT1 is determined.
 7. The method according to claim 4, whereinNEAT1 expression is evaluated by determining the presence ofparaspeckles.
 8. The method according to claim 5, wherein expression ofthe long isoform of NEAT1 is determined.
 9. The method according toclaim 5, wherein NEAT1 expression is evaluated by determining thepresence of paraspeckles.
 10. The method according to claim 3, whereinthe solid tumor is a carcinoma.
 11. The method according to claim 3,wherein the solid tumor is selected from the group consisting of breastcancer, skin cancer, osteosarcoma, colorectal cancer, and neuroblastoma.12. The method according to claim 3, wherein administration of thecombination-therefor selectively induces apoptosis in cancer cells inthe subject.
 13. A method of treating a subject diagnosed as having asolid tumor selected from the group consisting of breast cancer, skincancer, osteosarcoma, colorectal cancer, and neuroblastoma, the methodcomprising: inhibiting expression of NEAT1 in the subject byadministering the combination of claim 1 an inhibitor selected from thegroup consisting of an antisense oligonucleotide, an shRNA, and an siRNAthat is complementary to NEAT1 RNA in such a manner as to treat thesubject for the solid tumor.
 14. The combination of claim 1, wherein theantisense oligonucleotide comprises a locked nucleic acid (LNA), apeptide nucleic acid (PNA) or a morpholino.
 15. The combination of claim1, wherein the antisense oligonucleotide is a gapmer.
 16. The methodaccording to claim 3, wherein the antisense oligonucleotide comprises alocked nucleic acid (LNA), a peptide nucleic acid (PNA) or a morpholino.17. The method according claim 3, wherein the antisense oligonucleotideis a gapmer.
 18. The method according to claim 13, wherein the antisenseoligonucleotide comprises a locked nucleic acid (LNA), a peptide nucleicacid (PNA) or a morpholino.
 19. The method according claim 13, whereinthe antisense oligonucleotide is a gapmer.